Build/check report for BioC 3.24 - BIOCCHECK results for evaluomeR on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4890
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*
BIOCCHECK results for evaluomeR on nebbiolo2

To the developers/maintainers of the evaluomeR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/evaluomeR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
raw results
Summary

Package: evaluomeR
Version: 1.29.0
Command: /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('evaluomeR_1.29.0.tar.gz','quit-with-status'=TRUE)"
StartedAt: 2026-05-09 06:46:21 -0400 (Sat, 09 May 2026)
EndedAt: 2026-05-09 06:47:25 -0400 (Sat, 09 May 2026)
EllapsedTime: 64.1 seconds
RetCode: 0
Status: WARNINGS
CheckDir: None
Warnings: 2
Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('evaluomeR_1.29.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
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── Installing evaluomeR ────────────────────────────────────────────────────────
✔ Package installed successfully
── evaluomeR session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR
→ BiocVersion: 3.24
→ Package: evaluomeR
→ PackageVersion: 1.29.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/evaluomeR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR
→ installDir: /tmp/RtmpATigjP/file97b0dc66db6b
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on evaluomeR ──────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.6 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Coverage
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (8%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking package installation calls in R code...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/bioMetrics.Rd:18: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/ontMetrics.Rd:17: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/quality.Rd:63: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/qualityRange.Rd:69: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/qualitySet.Rd:65: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/rnaMetrics.Rd:18: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stability.Rd:59: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stability.Rd:61: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stabilityRange.Rd:62: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stabilityRange.Rd:64: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stabilitySet.Rd:60: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stabilitySet.Rd:62: unknown macro '\insertRef'
* Checking for library/require of evaluomeR...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/helpers.R (line 23, column 13)
    • ...
    • R/qualityIndices.R (line 793, column 18)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • helpers.R (line 118, column 13)
    • ...
    • stabilityIndex.R (line 633, column 112)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/helpers.R (line 169, column 14)
    • ...
    • print() in R/predictions.R (line 177, column 3)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/correlation.R (line 38, column 15)
    • ...
    • R/stabilityIndex.R (line 625, column 11)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/internalClusterboot.R (line 398, column 18)
    • ...
    • R/stabilityIndex.R (line 289, column 19)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/helpers.R (line 184, column 13)
    • ...
    • R/stabilityIndex.R (line 357, column 17)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • T in R/metricsAnalysis.R (line 795, column 64)
! WARNING: Remove set.seed usage (found 8 times)
  • set.seed() in R/internalClusterboot.R (line 617, column 23)
  • ...
  • set.seed() in R/predictions.R (line 63, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/internalFunctions.R (line 168, column 22)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 22 times)
  • suppressMessages() in R/metricsAnalysis.R (line 106, column 5)
  • ...
  • suppressWarnings() in R/stabilityIndex.R (line 191, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 22
functions greater than 50 lines.
  The longest 5 functions are:
    • clusterboot() (R/internalClusterboot.R): 290 lines
    • ...
    • getOptimalKValue() (R/metricsAnalysis.R): 122 lines
* Checking man page documentation...
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/bioMetrics.Rd:18: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/ontMetrics.Rd:17: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/quality.Rd:63: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/qualityRange.Rd:69: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/qualitySet.Rd:65: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/rnaMetrics.Rd:18: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stability.Rd:59: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stability.Rd:61: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stabilityRange.Rd:62: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stabilityRange.Rd:64: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stabilitySet.Rd:60: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stabilitySet.Rd:62: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/bioMetrics.Rd:18: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/ontMetrics.Rd:17: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/quality.Rd:63: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/qualityRange.Rd:69: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/qualitySet.Rd:65: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/rnaMetrics.Rd:18: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stability.Rd:59: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stability.Rd:61: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stabilityRange.Rd:62: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stabilityRange.Rd:64: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stabilitySet.Rd:60: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stabilitySet.Rd:62: unknown macro '\insertRef'
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • getMetricRangeByCluster.Rd
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/bioMetrics.Rd:18: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/ontMetrics.Rd:17: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/quality.Rd:63: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/qualityRange.Rd:69: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/qualitySet.Rd:65: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/rnaMetrics.Rd:18: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stability.Rd:59: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stability.Rd:61: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stabilityRange.Rd:62: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stabilityRange.Rd:64: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stabilitySet.Rd:60: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage, macros = rdmacros) :
  /tmp/RtmpATigjP/file97b0d4aa84793/evaluomeR/man/stabilitySet.Rd:62: unknown macro '\insertRef'
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 248 lines (5%) are > 80 characters long.
  First few lines:
    • R/correlation.R#L19 #' cor = metricsCorrelations(ontMetrics, ...
    • ...
    • vignettes/manual.Rmd#L426 REST^[[API documentation](https://docume ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2000 lines (40%) are
not.
  First few lines:
    • R/correlation.R#L23 data <- as.data.frame(assay(data)) ...
    • ...
    • vignettes/manual.Rmd#L372 scroll_box(width = "100%", height = "1 ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel
mailing list (requires admin credentials). Subscribe here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
ℹ Maintainer is registered at support site.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 18 NOTES
ℹ See the evaluomeR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.